Contacts of the strand formed by residues 232 - 236 (chain H) in PDB entry 1C1V
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 232 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187H CYS* 3.0 22.9 - - - -
188H ALA 3.1 14.7 + - - -
195H ASP* 3.9 8.1 + - - -
221H TRP 3.7 8.3 - - - -
222H GLY* 4.6 0.2 - - - -
231H TYR* 1.3 76.0 - - - +
233H PHE* 1.3 64.1 + - - -
234H TYR* 3.6 9.9 - - - -
410H BAB 3.7 18.8 - - - -
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Residues in contact with PHE 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H CYS* 4.1 12.8 - - + -
176H SER* 4.2 6.7 - - - -
177H THR* 4.1 11.9 - - + -
181H ILE* 3.2 37.7 - - + -
185H MET* 4.7 7.0 - - + -
186H PHE 3.4 12.6 - - - +
187H CYS* 3.8 17.0 - - + -
219H VAL* 4.5 1.2 - - - +
220H SER* 3.1 21.9 + - - -
221H TRP* 3.0 79.0 + + + +
223H GLU* 5.0 4.0 - - - -
231H TYR* 3.7 19.3 - - + -
232H GLY* 1.3 78.0 - - - -
234H TYR* 1.3 68.0 - - - +
410H BAB 5.3 0.9 + - - -
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Residues in contact with TYR 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H VAL* 3.7 20.6 - - + +
165H LEU* 3.8 14.6 - - - +
185H MET* 3.3 24.2 - - - +
186H PHE* 3.2 43.7 + + + -
188H ALA* 3.9 19.1 - - + -
195H ASP* 4.7 3.8 + - - -
196H ALA* 4.3 11.2 - - + +
205H PHE* 4.0 25.4 - + + -
218H ILE 3.0 26.9 - - - +
219H VAL* 3.7 28.3 - - + -
220H SER* 3.9 5.8 - - - -
232H GLY* 3.6 24.2 - - - -
233H PHE* 1.3 77.2 - - - +
235H THR* 1.3 62.6 + - - +
410H BAB 5.6 0.9 - - - -
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Residues in contact with THR 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H ARG* 4.7 1.1 - - - +
102H ASP* 2.9 45.8 + - - +
103H ILE* 4.5 3.6 - - + -
184H ASN 3.8 8.5 - - - +
185H MET* 4.7 1.1 - - - +
186H PHE* 3.9 1.4 - - - -
217H GLY* 3.2 25.6 - - - -
218H ILE* 3.0 27.1 + - + +
220H SER* 4.0 4.8 - - - -
234H TYR* 1.3 72.9 - - - +
236H HIS* 1.3 62.9 + - - +
237H VAL* 3.2 3.2 + - - +
240H LEU* 3.4 30.5 - - + -
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Residues in contact with HIS 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H ALA* 5.4 2.0 - - + -
130H LEU* 3.2 35.4 - - + +
170H ARG* 4.7 6.5 + - - -
183H ASP 3.7 16.8 - - - -
184H ASN* 3.1 28.4 + - - +
185H MET* 4.0 11.2 - - - +
186H PHE* 4.3 11.4 - + + +
216H MET 4.2 3.9 + - - -
234H TYR 3.7 1.0 + - - -
235H THR* 1.3 71.0 - - - +
237H VAL* 1.3 67.0 + - - +
238H PHE* 3.3 18.0 + + + -
239H ARG* 3.1 38.3 + - + +
240H LEU* 3.4 12.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il